title: IL10_Colon_CIF_Rep2_(Pool16)

status: Public on Dec 01 2008

city: Palmerston North

first: Matthew

last: Barnett

address: Grasslands Research Centre, Tennent Drive

country: New Zealand

institute: AgResearch

hyb_protocol: Microarray hybridization was performed according to a reference design without dye swap. The in situ hybridization kit-plus (Agilent Technologies Inc., Palo Alto, California, USA) was used to hybridize cRNA samples to Agilent Technologies Mouse G4121A - 44k 60mer oligonucleotide arrays. Cy3-labelled cRNA (sample, 0.75 µg) and Cy5-labelled cRNA (reference, 0.75 µg) were hybridised onto the microarray according to the manufacturer’s protocol. Following hybridisation, slides were washed in solutions I, II and III (Agilent Technologies, Santa Clara, CA, USA) and air-dried.

scan_protocol: Slides were scanned using a GenePix 4200A scanner (Molecular Devices Corporation, Sunnyvale, CA, USA) at a photomultiplier tube (PMT) setting of 450 V. Spot identification and quantification were performed using GenePix 6.0 software (Molecular Devices Corporation, Sunnyvale, CA, USA). Spot identification and quantification was performed using GenePix 6.0 software (Molecular Devices). All slides were individually checked and manually flagged for abnormalities.

data_processing:
Statistical analysis was performed using linear models for microarray analysis (limma) within the Bioconductor framework. Before analysis, poor quality spots were manually flagged and filtered out. Quality of the microarray data was assessed on diagnostic plots (boxplots and density plots) and spatial images generated from the raw (non-processed) data. All twenty arrays passed these strict criteria and were included in the analyses. Intensity ratio values for all microarray spots were normalized using a within-slide global Locally Weighted Scatterplot Smoothing (Loess) procedure to remove the effect of systematic variation in the microarrays; no background correction was necessary due to homogeneous hybridization. The normalized data from the arrays of each treatment group were averaged. For each comparison, differentially expressed genes were identified using false discovery rate (FDR) control with a threshold of q < 0.05. Data were log transformed before analysis and the mean difference between treatments calculated on this scale, resulting in a log ratio for each probe. The normalized values in the database consist of these log ratios. MA plots of the microarray data were drawn in order to check that there was no dependence of the log ratio on the intensity for any slide. The significance of the log ratio for each probe was determined by calculating one modified t-statistic per probe using an empirical Bayes approach.
The probability values were then corrected for multiple testing using the Benjamini and Hochberg correction, and a false discovery rate (FDR) calculated. Probes that had an FDR of less than 5 % (q<0.05) were considered to be differentially expressed between treatment.

source_name: Colon Tissue, CIF inoculated mouse

label_protocol: The Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies Inc., Palo Alto, California, USA) was used to synthesize cDNA and fluorescent cRNA. Labelled cRNA was made on the same day for all sample pools, including the reference sample. cDNA was synthesized from 500 ng of purified total RNA from each pool using T7 promotor primer and Moloney Murine Leukemia Virus Reverse Transcriptase according to the manufacturer’s protocol. Cy3 (PerkinElmer, Waltham, Massachusetts 02451, USA) was used to label sample groups, while the reference RNA was labeled with Cy5 (PerkinElmer, Waltham, Massachusetts 02451, USA).

growth_protocol: Mice were weighed three times a week throughout the experiment to determine body weight changes. To minimize variation in the time interval between the last food intake and tissue sampling, mice were fasted overnight on the night before sampling. On the morning of sampling, food was returned for two hours, followed by a further two hour fast immediately prior to tissue sampling. Blood was collected from euthanised mice by cardiac puncture. Plasma was separated from red blood cells by centrifugation (2000 g, 10 min, 4 ºC), frozen in liquid nitrogen and stored at - 80 ºC. The intestine was removed, cut open lengthwise and flushed with 0.9 % NaCl to remove digesta residues. The proximal half of the colon was cut in two pieces, one for histological evaluation and other for gene expression studies. Samples of the colon tissue for gene expression analysis were frozen in liquid nitrogen and stored at - 80 ºC. Samples for histological analysis were stored in formalin solution (10 % neutral buffered) at room temperature.

extract_protocol: Total RNA was extracted from the colon tissues using Trizol (Invitrogen, Carlsbad, CA, USA) as described by the manufacturer, with a subsequent purification step using RNeasy columns (Qiagen, San Diego, CA, USA). RNA was quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and RNA quality was examined using a RNA 6000 LabChip Kit and a 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol:
Animals. Twenty five male IL-10-/- (C57BL/6J background, formal designation B6.129P2-IL-10<tm1Cgn>/J) mice and twenty five male C57BL/6J (C57) control mice were received from The Jackson Laboratory (Bar Harbor, Maine, USA) at approximately five weeks of age. Mice were housed either in pairs or groups of three (5 mice per treatment) in shoebox-style cages containing untreated wood shavings and a plastic tube for environmental enrichment. The animal room was maintained at a temperature of ~22°C and humidity of ~50% with a 12 hour light/dark cycle. All mice had ad libitum access to water, which was refreshed twice a week. An AIN-76A powdered diet was supplied twice a week, with sufficient provided to meet the daily intake of IL-10-/- mice, as determined in a previous feeding trial (data not shown). The diet for all groups was sterilized by gamma irradiation (Schering-Plough, Wellington, New Zealand) to a level required for SPF conditions, to minimize the possibility of bacterial introduction to the SPF group of animals. All mice were weighed twice weekly and carefully monitored for disease symptoms (weight loss, soft faeces and inactivity).
Experimental design. Both IL-10-/- and C57 mice were randomly divided into five treatment groups with five animals per group.
1. SPF. Housed in Specific Pathogen Free (SPF) conditions (isolator cages supplied with HEPA filtered air (Tecniplast SpA, Buguggiate, Italy)).
2. C. Maintained under conventional conditions.
3. EF. Maintained under conventional conditions and orally inoculated (200 microlitres) with a solutions containing 12 pure strains of Enterococcus (1.2 x 108 colony forming units (CFU)).
4. CIF. Maintained under conventional conditions and orally inoculated with conventional intestinal flora (CIF) derived from healthy age-matched C57BL/6 mice which had been raised under conventional conditions. The CIF inoculation protocol was included to better mimic the complete microbiota associated with the mouse gastrointestinal tract.
5. EF.CIF. Maintained under conventional conditions and orally inoculated with a combination of the EF and CIF inoculation solutions (6.0 x 107 CFU from the EF inoculum).
Preparation of EF bacterial solutions for oral inoculation. Seventy two hours prior to inoculation, colonies of the E. faecalis and E. faecium strains were sub-cultured from slope tubes onto fresh Slanetz & Bartley medium (Oxoid, Hampshire, UK), and incubated at 42°C for 48 h. A single colony from each culture was subsequently transferred to 5 mL of Todd Hewitt Broth (Oxoid, Hampshire, UK), and incubated at 37°C for 24 h. Each Enterococcus culture was centrifuged to pellet the bacterial cells (3,000 g, 10 min, 4°C), which were then re-suspended in 5 mL sterile PBS (pH 7.4) and pooled (EF inoculum).
Preparation of CIF bacterial solutions for oral inoculation. The healthy, age-matched C57BL/6 mice from which flora were being collected were humanely euthanized by CO2 asphyxiation and cervical dislocation and the gastrointestinal tract (from stomach to just below the caecum) removed. Digesta were collected from the intestine and caecum by gently washing with sterile PBS, pH 7.4, then suspended in a total of 30 mL PBS. After mixing by gentle inversion and a settling period of approximately 5 min, the suspension was collected (CIF inoculum). Inoculation solutions EF and CIF were mixed in a 1:1 (v/v) solution to obtain the EF.CIF inoculum.

tag: Strain

tag: Gender

value: male

tag: Age

value: 5 weeks of age at the start of the experiment, 12 weeks of age when tissue samples taken

tag: Tissue

value: colon tissue

source_name: Reference Pooled Sample of colon RNA

label_protocol: As per Channel 1

growth_protocol: As per Channel 1

extract_protocol: As per Channel 1

treatment_protocol: As per Channel 1

value: IL10-/- and C57BL/6J

value: 12 weeks

tag: Reference sample consisted of RNA extracted from colon tissue of all mice in this experiment (both IL10-/- and C57BL/6J) pooled in equimolar amounts.


title: S2 cell culture 3 replicate 2 at time 1h post Buchnera aphidicola APS infection

status: Public on Dec 15 2008

type: RNA

city: Cambridge

first: Roslin

last: Russell

address: Downing Street

department: Department of Genetics

country: United Kingdom

institute: University of Cambridge

hyb_protocol: Hybridisation to amino-modified long oligonucleotide microarrays using a Genomic Solutions hybridisation station with the Biosolutions hybridisation buffer (http://www.flychip.org.uk/protocols/hybridisation/hyb_oligoMWG.pdf)

scan_protocol: Operating instructions for the Genepix 4000B dual laser scanner (http://www.flychip.org.uk/protocols/imaging/scanning2.pdf

data_processing: Spot finding and quantitation via the Dapple package.

molecule: total RNA

organism: Drosophila melanogaster

source_name: pool

label_protocol: Reverse transcription and direct labelling for cDNA and oligo arrays (http://www.flychip.org.uk/protocols/gene_expression/direct_labelling.pdf) using 40ug of total RNA.

growth_protocol: Drosophila melanogaster S2 cells experimentally growing in Schneider's Drosophila medium supplemented with 10% foetal calf serum.

extract_protocol: Medium scale Trizol extraction (http://www.flychip.org.uk/protocols/gene_expression/standard_extraction.pdf).

tag: pool of S2 cells not exposed to Buchnera aphidicola APS

extract_protocol: Medium scale Trizol extraction (http://www.flychip.org.uk/protocols/gene_expression/medium_extraction.php).


title: S2 cell culture 4 replicate 1 at time 6h post Buchnera aphidicola APS infection


title: S2 cell culture 1 replicate 1 at time 1h post Buchnera aphidicola APS infection


title: S2 cell culture 2 replicate 2 at time 6h post Buchnera aphidicola APS infection


title: S2 cell culture 1 replicate 2 at time 1h post Buchnera aphidicola APS infection


title: C57BL/6J_Colon_CIF_Rep2_(Pool14)

organism: Mus musculus

value: C57BL/6J mice (control)


title: E13ENP biological replicate 3

city: Bethesda

first: Joe

middle: A

last: Nielsen

state: MD

address: 49 Convent Drive BD49,5A75

country: USA

institute: NIH/NINDS

description: Flow cytometry was used to isolate tetanus toxin+ and cholera toxin+ neuronal progenitors from embryonic days 11, 12 and 13 rat telencephalon.

hyb_protocol: Affymetrix standard protocols were followed using the hybridization oven 640, and washing with the fluidics station 450

scan_protocol: The microarrays were scanned with a genechip scanner 3000 7G

data_processing: Cel files were imported into Genespring for preprocessing using RMA, and normalization using a global per-chip and per-gene normalization strategy

label: Biotin

organism: Rattus norvegicus

source_name: Embryonic day 13 early neuronal progenitors

label_protocol: Affymetrix small sample labeling protocol

extract_protocol: Qiagen's RNeasy micro kit

tag: E13 neuronal progenitors positively selected with tetanus toxin and cholera toxin using flow cytometry


title: C57BL/6J_Colon_EF_Rep1_(Pool9)

source_name: Colon Tissue, Enterococcus inoculated mouse

value: C57BL/6J mice


title: IL10_Colon_Conventional_Rep2_(Pool8)

source_name: Colon Tissue, Conventional Conditions


title: IL10_Colon_EF_Rep2_(Pool12)


title: IL10_Colon_EF_Rep1_(Pool11)


title: C57BL/6J_Colon_CIF_Rep1_(Pool13)


title: C57BL/6J_Colon_EF_Rep2_(Pool10)


title: E13LNP biological replicate 2

source_name: Embryonic day 13 late neuronal progenitors

tag: E13 neuronal progenitors positively selected with tetanus toxin and cholera toxin using flow cytometry (tetanus toxin and cholera toxin high)


title: E12ENP biological replicate 3

source_name: Embryonic day 12 early neuronal progenitors

tag: E12 neuronal progenitors positively selected with tetanus toxin and cholera toxin using flow cytometry


title: E13LNP biological replicate 1


title: IL10_Colon_CIF_Rep1_(Pool15)


title: C57BL/6J_Colon_Conventional_Rep2_(Pool6)


title: E13LNP biological replicate 3


title: E13ENP biological replicate 2


title: IL10_Colon_Conventional_Rep1_(Pool7)


title: d14E vs. d7 placebo (REP2, HYB2)

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Frozen mammary gland tissue, collected from four to five mice at day seven (placebo) or day 14 (estradiol), was pooled and RNA was prepared using Trizol reagent and the RNeasy clean up protocol.

data_processing: Five hundred ng of total RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's protocol.  For each two color comparison, 750 ng of each Cy3- and Cy5-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing and scanning with an Agilent Scanner.  Data was obtained using the Agilent Feature Extraction software (v8.1), using default for all parameters.

source_name: d7 placebo (Cy5)

tag: d7 placebo


title: E11ENP biological replicate 4

source_name: Embryonic day 11 early neuronal progenitors

tag: E11 neuronal progenitors positively selected with tetanus toxin and cholera toxin using flow cytometry


title: E12ENP biological replicate 4


title: C57BL/6J_Colon_Conventional_Rep1_(Pool5)


title: E13ENP biological replicate 4


title: E12ENP biological replicate 2


title: IL10_Colon_SPF_Rep2_(Pool4)

source_name: Colon Tissue, SPF Conditions


title: E11ENP biological replicate 2


title: d5E vs. d7 placebo (HYB2)

description: Frozen mammary gland tissue, collected from four to five mice at day seven (placebo) or day five (estradiol), was pooled and RNA was prepared using Trizol reagent and the RNeasy clean up protocol.

source_name: d5E (Cy3)


title: C57BL/6J_Colon_SPF_Rep1_(Pool1)


title: wk4E vs. d7 placebo (REP2, HYB2)

description: Frozen mammary gland tissue, collected from four to five mice at day seven (placebo) or week 4 (estradiol), was pooled and RNA was prepared using Trizol reagent and the RNeasy clean up protocol.

source_name: wk4E (Cy3)


title: E12ENP biological replicate 1


title: IL10_Colon_SPF_Rep1_(Pool3)


title: C57BL/6J_Colon_SPF_Rep2_(Pool2)


title: E13ENP biological replicate 1


title: d7 placebo vs. d14E (REP2, HYB1)

source_name: d7 placebo (Cy3)


title: d7E vs. d7 placebo (REP2, HYB2)

description: Frozen mammary gland tissue, collected from four to five mice at day seven (placebo) or day seven (estradiol), was pooled and RNA was prepared using Trizol reagent and the RNeasy clean up protocol.

source_name: d7E (Cy3)


title: 7C424-HB3_18hpi

status: Public on Nov 20 2008

city: Notre Dame

first: Michael

last: Ferdig

state: IN

address: 280 Galvin Life Science

department: Biological Sciences

institute: University of Notre Dame

description: Dd2/progeny test samples co-hybridized with a common HB3 reference; all samples extracted at 18 hours post RBC invasion after sorbitol cell synchronization; parasites cultured using standard culture conditions in O+ blood and albumax

hyb_protocol: Samples were hybridized following previously implemented protocols (Bozdech Z, et al. PLoS Biology. 2003)

scan_protocol: Slides were scanned in an Axon GenePix 4000B microarray scanner (Axon Instruments, Inc.; Union City, California) with 532 nm (17 mW) and 635 nm (10 mW) lasers. Data was collected as an image file, gridded, and converted into a text file using Genepix 3.0 software (Axon Instruments, Inc.; Union City, California).

data_processing: Lowess smoothing of the raw expression data was used to normalize across all microarray slides using TIGR’s MultiExperiment Viewer (MeV) v4.0 and Microarray Data Analysis System (MIDAS) v2.19 software (available < http://www.tm4.org>). Gene expression values are reported as log2(sample/HB3 reference) of each normalized fluorescent signal.

organism: Plasmodium falciparum

source_name: Parasite culture, 7C424 progeny clone, 18 hours post RBC invasion

label_protocol: cDNA was synthesized and labeled using the Ovation Aminoallyl RNA Amplification and Labeling Kit (cat. # 2101-12; NuGEN Technologies, Inc., San Carlos, California).

growth_protocol: Parasites cultured using standard techniques (Trager & Jansen. Science. 1976), in O+ human blood and albumax-based media.

extract_protocol: Total RNA extracted using TRIzol reagent following manufacturer's instructions

treatment_protocol: 5% Sorbitol treatment used twice in subsequent life cycles to synchronize parasites.

tag: Sorbitol synchronized parasite cultures

source_name: Parasite culture, HB3 parent clone, 18 hours post RBC invasion


title: d7 placebo vs. d2E (HYB1)

description: Frozen mammary gland tissue, collected from four to five mice at day seven (placebo) or day two (estradiol), was pooled and RNA was prepared using Trizol reagent and the RNeasy clean up protocol.

source_name: d2E (Cy5)


title: E11ENP biological replicate 3


title: E11ENP biological replicate 1

tag: E11 neuronal progenitors positively selected with tetanus toxin and cholara toxin using flow cytometry


title: d2E vs. d7 placebo (HYB2)

source_name: d2E (Cy3)


title: d7 placebo vs. wk4E (REP2, HYB1)

source_name: wk4E (Cy5)


title: WK1-placebo vs. WK4-E (REP1, HYB1)

data_processing: Five hundred ng of total RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's protocol.  For each two color comparison, 750 ng of each Cy3- and Cy5-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing and scanning with an Agilent Scanner.  Data was obtained using the Agilent Feature Extraction software (v7.5), using default for all parameters.

source_name: WK1-placebo (Cy3)

source_name: WK4-E (Cy5)


title: 7C421-HB3_18hpi

source_name: Parasite culture, 7C421 progeny clone, 18 hours post RBC invasion


title: 7C159-HB3_18hpi

source_name: Parasite culture, 7C159 progeny clone, 18 hours post RBC invasion


title: WK1-placebo vs. WK2-E (REP1, HYB1)

source_name: WK2-E (Cy5)


title: d7 placebo vs. d7E (REP2, HYB1)

source_name: d7E (Cy5)


title: 7C183-HB3_18hpi

source_name: Parasite culture, 7C183 progeny clone, 18 hours post RBC invasion


title: 7C170-HB3_18hpi

source_name: Parasite culture, 7C170 progeny clone, 18 hours post RBC invasion


title: WK2-E vs. WK1-placebo (REP1, HYB2)

source_name: WK2-E (Cy3)

source_name: WK1-placebo (Cy5)


title: WK4-E vs. WK1-placebo (REP1, HYB2)

source_name: WK4-E (Cy3)


title: GC06-HB3_18hpi

source_name: Parasite culture, GC06 progeny clone, 18 hours post RBC invasion


title: d7 placebo vs. d5E (HYB1)

source_name: d7 placebo (Cy3)

source_name: d5E (Cy5)


title: 7C126-HB3_18hpi

source_name: Parasite culture, 7C126 progeny clone, 18 hours post RBC invasion

source_name: Parasite culture, HB3 parent clone, 18 hours post RBC invasion


title: 7C20-HB3_18hpi

source_name: Parasite culture, 7C20 progeny clone, 18 hours post RBC invasion


title: 7C46-HB3_18hpi

source_name: Parasite culture, 7C46 progeny clone, 18 hours post RBC invasion


title: 7C111-HB3_18hpi

source_name: Parasite culture, 7C111 progeny clone, 18 hours post RBC invasion


title: 7C16-HB3_18hpi

source_name: Parasite culture, 7C16 progeny clone, 18 hours post RBC invasion


title: QC23-HB3_18hpi

source_name: Parasite culture, QC23 progeny clone, 18 hours post RBC invasion


title: 7C140-HB3_18hpi

source_name: Parasite culture, 7C140 progeny clone, 18 hours post RBC invasion


title: WK1-placebo vs. WK1-E (REP1, HYB1)

source_name: WK1-placebo (Cy3)

source_name: WK1-E (Cy5)


title: TC05-HB3_18hpi

source_name: Parasite culture, TC05 progeny clone, 18 hours post RBC invasion


title: D43-HB3_18hpi

source_name: Parasite culture, D43 progeny clone, 18 hours post RBC invasion


title: 7C12-HB3_18hpi

source_name: Parasite culture, 7C12 progeny clone, 18 hours post RBC invasion


title: CH3-61-HB3_18hpi

source_name: Parasite culture, CH3-61 progeny clone, 18 hours post RBC invasion


title: SC01-HB3_18hpi

source_name: Parasite culture, SC01 progeny clone, 18 hours post RBC invasion


title: 7C408-HB3_18hpi

source_name: Parasite culture, 7C408 progeny clone, 18 hours post RBC invasion


title: 3BA6-HB3_18hpi

source_name: Parasite culture, 3BA6 progeny clone, 18 hours post RBC invasion


title: QC34-HB3_18hpi

source_name: Parasite culture, QC34 progeny clone, 18 hours post RBC invasion


title: 3BD5-HB3_18hpi

source_name: Parasite culture, 3BD5 progeny clone, 18 hours post RBC invasion

source_name: Parasite culture, HB3 parent clone, 18 hours post RBC invasion


title: 7C7-HB3_18hpi

source_name: Parasite culture, 7C7 progeny clone, 18 hours post RBC invasion


title: 7C3-HB3_18hpi

source_name: Parasite culture, 7C3 progeny clone, 18 hours post RBC invasion


title: HB3-HB3_18hpi

source_name: Parasite culture, HB3 progeny clone, 18 hours post RBC invasion


title: SC05-HB3_18hpi

source_name: Parasite culture, SC05 progeny clone, 18 hours post RBC invasion


title: CH3-116-HB3_18hpi

source_name: Parasite culture, CH3-116 progeny clone, 18 hours post RBC invasion


title: Dd2-HB3_18hpi

source_name: Parasite culture, Dd2 parent clone, 18 hours post RBC invasion


title: 1BB5-HB3_18hpi

source_name: Parasite culture, 1BB5 progeny clone, 18 hours post RBC invasion


title: B4R3-HB3_18hpi

source_name: Parasite culture, B4R3 progeny clone, 18 hours post RBC invasion


title: 7C188-HB3_18hpi

source_name: Parasite culture, 7C188 progeny clone, 18 hours post RBC invasion


title: QC01-HB3_18hpi

source_name: Parasite culture, QC01 progeny clone, 18 hours post RBC invasion


title: TC08-HB3_18hpi

source_name: Parasite culture, TC08 progeny clone, 18 hours post RBC invasion


title: QC13-HB3_18hpi

source_name: Parasite culture, QC13 progeny clone, 18 hours post RBC invasion


title: GC03-HB3_18hpi

source_name: Parasite culture, GC03 progeny clone, 18 hours post RBC invasion


title: Double Mutant (agr and codY) versus reference pool (replicate #2)

status: Public on Nov 07 2008

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

description: Comparison of newman agr mutant Versus S.aureus pool

hyb_protocol: Labelled products were then purified onto QiaQuick columns (Qiagen). Labelled cDNA mixture was diluted in 50 µl Agilent hybridization buffer, and hybridized at a temperature of 60°C for 17 hours

scan_protocol: Slides were dried under nitrogen flow, and scanned using 100% Photon Multiplier Tube (PMT) power for both wavelengths using Agilent scanner.

data_processing: Lowess on Background subtracted value

organism: Staphylococcus aureus subsp. aureus str. Newman

source_name: Double Mutant (agr and codY)

label_protocol: Batches of 5 µg total S. aureus RNA were labelled by Cy3dCTP (wild-type strain) or with Cy5 dCTP (mutant strains) using the SuperScript II  following manufacturer's instructions.

extract_protocol: Total RNA was purified from bacteria grown in CDM to an OD600 = 0.5; Trizol (Invitrogen) was used for purification and RNeasy (Qiagen) for cleaning.  After additional DNase treatment, the absence of remaining DNA traces was evaluated by quantitative PCR with assays specific for 16s rRNA.

tag: Staphylococcus aureus Newman, Double Mutant (agr and codY)

organism:
Staphylococcus aureus subsp. aureus NCTC 8325
Staphylococcus aureus subsp. aureus COL
Staphylococcus aureus subsp. aureus Mu50
Staphylococcus aureus subsp. aureus N315
Staphylococcus aureus subsp. aureus MW2
Staphylococcus aureus subsp. aureus MRSA252
Staphylococcus aureus subsp. aureus MSSA476
Staphylococcus aureus subsp. aureus USA300

source_name: S.aureus reference pool

tag: S.aureus reference pool (N315, COL, MRSA252, MSSA476, Mu50, MW2, NCTC8325 and USA300 )


title: B1SD-HB3_18hpi

source_name: Parasite culture, B1SD progeny clone, 18 hours post RBC invasion


title: T1Cy3_T1ECy5_rep1

status: Public on Nov 01 2008

city: Braga

first: Pedro

middle: M. R.

last: Guimaraes

address: Campus de Gualtar

department: Department of Biological Engineering

country: Portugal

institute: University of Minho - CEB

description: Biological replicate 1 of 4 with dye switch. The evolved strain T1-E is a derivative of the original lactose-consuming Saccharomyces cerevisiae recombinant strain T1, obtained by a long-term evolutionary engineering experiment described by Guimarães et al. (2008) [Appl Environ Microbiol 74:3076-3084].

hyb_protocol: Hybridization was carried out in an automatic hybridation chamber (Discovery™, Ventana). Microarrays were prehybridized in a solution of 1% BSA, 2x SCC, 0.2% SDS for 30 min at 42ºC, followed by prehybridization for 30min with the Chip Prep 1 reagent (Ventana) then 30 min with the Chip Prep 2 reagent (Ventana) at 42°C. Hybridization was done by addition of a mixture containing 180 µl of ChipHybe™ (Ventana), 10 µl of Cy3-labelled cDNA and 10 µl of Cy5-labelled cDNA. After 8 h of hybridization at 42ºC, the DNA chips were washed with the ChipClean (Ventana) solution. All of those steps were done automatically in the hybridization chamber. Subsequently the slides were washed manually for 5 min in a 2x SSC, 0,1% SDS solution, then for 2 min in 0.1x SSC buffer at room temperature. Finally the slides were dried with a microarray high-speed centrifuge (ArrayIt).

scan_protocol: The hybridization signal was detected by scanning the microarrays with a GenePix 4000A laser scanner (Axon Instruments) and quantified using the accompanying GenePix Pro 6.0 software.

data_processing: LOWESS normalized, background (local background) subtracted VALUE data obtained from log of processed Red signal / processed Green signal; lowest value limit = 10 (to prevent that a spot intensity become zero or negative after the background subtraction)"

organism: Saccharomyces cerevisiae

source_name: Total RNA from Saccharomyces cerevisiae recombinant strain T1 labeled with Cyanine-3 (green)

label_protocol: Synthesis of fluorescently labeled cDNA was carried out with 5 ng of total RNA using the ChipShot™ direct labeling system from Promega then purified with the ChipShot™ Labeling and Cleanup System. This labeling method allows direct incorporation of dCTP-Cy3 or dCTP-Cy5 (Perkin-Elmer) nucleotides during the reverse transcription step. The quality of the labeled cDNA was verified by the NanoDrop® ND-1000 UV-Vis Spectrophotometer.

growth_protocol: Yeast was grown to an OD600 of 0.5-0.7 in the yeast defined mineral medium described by Verduyn et al. (1992) [Yeast 8:501-517] with 20 g/L of lactose. The concentrations of trace elements and vitamins were doubled and the medium was supplemented with 100 mM potassium hydrogen phthalate to avoid major drops in pH during cultivation. Initial pH was adjusted to 4.5 with NaOH; the final pH was > 3.7. Cultivations were carried out in 250 mL Erlenmeyer flasks filled with 100 mL of medium and shaken (150 rpm) at 30 ºC. Preinocula were grown in the same conditions and used to inoculate the main cultures to an initial OD600 of about 0.05."

extract_protocol: Yeast cells for total RNA isolation were grown to an OD600 of 0.5 to 0.7. A volume correspondent to 15 OD600 x mL of culture was rapidly centrifuged (1050 x g at 4 ºC for 3 min) and the cell pellets were immediately frozen in liquid nitrogen and stored at -80 ºC. The cells were mechanically disrupted using a ball mill (Mikro-Dismembrator S, B. Braun Biotech International). Total RNA was extracted using RNeasy Mini kit (Qiagen). The extracted RNA was quantified using the Bioanalyzer 2100 with the RNA 6000 Nano LabChip kit (Agilent), and the NanoDrop ND-1000 UV/Vis spectrophotometer (NanoDrop Technologies).

tag: Lactose-consuming Saccharomyces cerevisiae, original recombinant, strain T1

source_name: Total RNA from Saccharomyces cerevisiae recombinant strain T1-E labeled with Cyanine-5 (red)

tag: Lactose-consuming Saccharomyces cerevisiae, evolved recombinant, strain T1-E


title: Wild-type S.aureus strain Newman versus reference pool (replicate #2)

source_name: Wild-type S.aureus strain Newman

tag: Staphylococcus aureus Newman,  Wild-type


title: Wild-type S.aureus strain Newman versus reference pool (replicate #1)


title: agr Mutant versus reference pool (replicate #1)

source_name: agr mutant

tag: Staphylococcus aureus Newman, agr mutant


title: Double Mutant (agr and codY) versus reference pool (replicate #1)

tag: Staphylococcus aureus Newman, Double Mutant (agr and codY).


title: T1Cy3_T1ECy5_rep2

description: Biological replicate 2 of 4 with dye switch. The evolved strain T1-E is a derivative of the original lactose-consuming Saccharomyces cerevisiae recombinant strain T1, obtained by a long-term evolutionary engineering experiment described by Guimarães et al. (2008) [Appl Environ Microbiol 74:3076-3084].


title: codY Mutant versus reference pool (replicate #2)

source_name: codY mutant

tag: Staphylococcus aureus Newman, codY mutant


title: T1Cy5_T1ECy3_rep3

description: Biological replicate 3 of 4 with dye switch. The evolved strain T1-E is a derivative of the original lactose-consuming Saccharomyces cerevisiae recombinant strain T1, obtained by a long-term evolutionary engineering experiment described by Guimarães et al. (2008) [Appl Environ Microbiol 74:3076-3084].

data_processing: LOWESS normalized, background (local background) subtracted VALUE data obtained from log of processed Green signal / processed Red signal; lowest value limit = 10 (to prevent that a spot intensity become zero or negative after the background subtraction)"

source_name: Total RNA from Saccharomyces cerevisiae recombinant strain T1 labeled with Cyanine-5 (red)

source_name: Total RNA from Saccharomyces cerevisiae recombinant strain T1-E labeled with Cyanine-3 (green)


title: T1Cy5_T1ECy3_rep4

description: Biological replicate 4 of 4 with dye switch. The evolved strain T1-E is a derivative of the original lactose-consuming Saccharomyces cerevisiae recombinant strain T1, obtained by a long-term evolutionary engineering experiment described by Guimarães et al. (2008) [Appl Environ Microbiol 74:3076-3084].


title: codY Mutant versus reference pool (replicate #1)


title: agr Mutant versus reference pool (replicate #2)


title: ChIP-chip time-course of H3K4me3 during meiosis (mutant Spo11F, t=4h)

type: genomic

city: New York

first: Nicolas

last: Robine

state: NY

address: 101 Avenue of the Americas

department: Bioinformatics

institute: New York Genome Center

description: Time-course of the trimethylation of the Lysine4 of Histone H3 during meiosis in a mutant Spo11F

hyb_protocol: 16 hours at 65°C in the 1X hybridization buffer supplied by Agilent

scan_protocol: Axon 4000B scanner. GenePix5.1 software

data_processing: Log2Ratios of background-corrected Intensities, spatial bias normalized with MANOR (Neuvial et al. 2006 Bioinformatics) mean fitted to 0. Then, we calculated for each time-point the average value of the ratios for probes located between 0 and 500 bp  of all the ORFs present on the array. Next, we calculated the average value of this peak during the whole time-course, and normalized the ratios of each array such that each array has now this average peak value.

molecule: genomic DNA

source_name: IP of H3K4me3 (mutant Spo11F, t=4h in meiosis)

label_protocol: two-thirds of the immunoprecipitated DNA was amplified by random primer extension followed by PCR amplification, incorporating amino-allyl dUTP for subsequent dye coupling

growth_protocol: For sporulation, cells were grown in rich medium (YPD) for 24h, then transferred into SPS pre-sporulation medium and grown overnight to ~4.107 cells/ml. Cells were then harvested by centrifugation, washed with one volume 1% potassium acetate and resuspended into sporulation medium (1% potassium acetate, 1/1000 polypropylene glycol 2000, 20µg/ml uracil) at a density of 2.107 cells/ml (t=4h).

extract_protocol: 20ml (4*108 cells) were crosslinked with 1% freshly prepared formaldehyde for 15 min at room temperature, then the reaction was stopped by the addition of 125mM glycin for 5 min. Cells were washed twice with cold TBS, and then chromatin immunoprecipitation was performed as described (Robine et al., 2007), using 3µl of rabbit polyclonal anti-triMe H3K4 (Abcam #Ab8580) and 30 µl protein G magnetic beads suspension (Dynal).

tag: Strain ORD7341

tag: t=4h after meiosis induction

source_name: Whole-cell extract

label_protocol: 1/70 of the DNA from the whole-cell extract was amplified by random primer extension followed by PCR amplification, incorporating amino-allyl dUTP for subsequent dye coupling

extract_protocol: 20ml (4*108 cells) were crosslinked with 1% freshly prepared formaldehyde for 15 min at room temperature, then the reaction was stopped by the addition of 125mM glycin for 5 min. Cells were washed twice with cold TBS and lyzed in ChIP lysis buffer.


title: ChIP-chip time-course of H3K4me3 during meiosis (mutant clb5Delta-clb6Delta, t=0h)

description: Time-course of the trimethylation of the Lysine4 of Histone H3 during meiosis in a mutant clb5Delta-clb6Delta

data_processing: Log2Ratios of background-corrected Intensities, spatial bias normalized with MANOR (Neuvial et al. 2006 Bioinformatics) mean fitted to 0. Then, we calculated for each time-point the average value of the ratios for probes located between 0 and 500 bp of all the ORFs present on the array. Next, we calculated the average value of this peak during the whole time-course, and normalized the ratios of each array such that each array has now this average peak value.

source_name: IP of H3K4me3 (mutant clb5Delta-clb6Delta, t=0h in meiosis)

growth_protocol: For sporulation, cells were grown in rich medium (YPD) for 24h, then transferred into SPS pre-sporulation medium and grown overnight to ~4.107 cells/ml. Cells were then harvested by centrifugation, washed with one volume 1% potassium acetate and resuspended into sporulation medium (1% potassium acetate, 1/1000 polypropylene glycol 2000, 20µg/ml uracil) at a density of 2.107 cells/ml (t=0h).

tag: Strain ORD6830

tag: t=0h after meiosis induction


title: ChIP-chip time-course of H3 occupancy during meiosis (mutant Spo11F, t=1h)

description: Time-course of Histone H3 occupancy during meiosis in a mutant Spo11F

data_processing: Log2Ratios of background-corrected Intensities, spatial bias normalized with MANOR (Neuvial et al. 2006 Bioinformatics) mean fitted to 0 and normalized to the same standard deviation.

source_name: IP of H3 occupancy (mutant Spo11F, t=1h in meiosis)

growth_protocol: For sporulation, cells were grown in rich medium (YPD) for 24h, then transferred into SPS pre-sporulation medium and grown overnight to ~4.107 cells/ml. Cells were then harvested by centrifugation, washed with one volume 1% potassium acetate and resuspended into sporulation medium (1% potassium acetate, 1/1000 polypropylene glycol 2000, 20µg/ml uracil) at a density of 2.107 cells/ml (t=1h).

extract_protocol: 20ml (4*108 cells) were crosslinked with 1% freshly prepared formaldehyde for 15 min at room temperature, then the reaction was stopped by the addition of 125mM glycin for 5 min. Cells were washed twice with cold TBS, and then chromatin immunoprecipitation was performed as described (Robine et al., 2007), using 3µl of rabbit polyclonal anti H3Cter (Abcam #1791) and 30 µl protein G magnetic beads suspension (Dynal).

tag: t=1h after meiosis induction

extract_protocol: 20ml (4*108 cells) were crosslinked with 1% freshly prepared formaldehyde for 15 min at room temperature, then the reaction was stopped by the addition of 125mM glycin for 5 min. Cells were washed twice with cold TBS and lyzed in ChIP lysis buffer


title: ChIP-chip time-course of H3K4me3 during meiosis (mutant clb5Delta-clb6Delta, t=3h)

source_name: IP of H3K4me3 (mutant clb5Delta-clb6Delta, t=3h in meiosis)

growth_protocol: For sporulation, cells were grown in rich medium (YPD) for 24h, then transferred into SPS pre-sporulation medium and grown overnight to ~4.107 cells/ml. Cells were then harvested by centrifugation, washed with one volume 1% potassium acetate and resuspended into sporulation medium (1% potassium acetate, 1/1000 polypropylene glycol 2000, 20µg/ml uracil) at a density of 2.107 cells/ml (t=3h).

tag: t=3h after meiosis induction


title: ChIP-chip time-course of H3 occupancy during meiosis (mutant Spo11F, t=0h)

source_name: IP of H3 occupancy (mutant Spo11F, t=0h in meiosis)


title: ChIP-chip time-course of H3K4me3 during meiosis (mutant clb5Delta-clb6Delta, t=6h)

source_name: IP of H3K4me3 (mutant clb5Delta-clb6Delta, t=6h in meiosis)

growth_protocol: For sporulation, cells were grown in rich medium (YPD) for 24h, then transferred into SPS pre-sporulation medium and grown overnight to ~4.107 cells/ml. Cells were then harvested by centrifugation, washed with one volume 1% potassium acetate and resuspended into sporulation medium (1% potassium acetate, 1/1000 polypropylene glycol 2000, 20µg/ml uracil) at a density of 2.107 cells/ml (t=6h).

tag: t=6h after meiosis induction


title: ChIP-chip time-course of H3K4me3 during meiosis (mutant Spo11F, t=3h)

source_name: IP of H3K4me3 (mutant Spo11F, t=3h in meiosis)


title: ChIP-chip time-course of H3K4me3 during meiosis (mutant clb5Delta-clb6Delta, t=2h)

source_name: IP of H3K4me3 (mutant clb5Delta-clb6Delta, t=2h in meiosis)

growth_protocol: For sporulation, cells were grown in rich medium (YPD) for 24h, then transferred into SPS pre-sporulation medium and grown overnight to ~4.107 cells/ml. Cells were then harvested by centrifugation, washed with one volume 1% potassium acetate and resuspended into sporulation medium (1% potassium acetate, 1/1000 polypropylene glycol 2000, 20µg/ml uracil) at a density of 2.107 cells/ml (t=2h).

tag: t=2h after meiosis induction


title: ChIP-chip time-course of H3K4me3 during meiosis (mutant Spo11F, t=0h)

source_name: IP of H3K4me3 (mutant Spo11F, t=0h in meiosis)


title: ChIP-chip time-course of H3 occupancy during meiosis (mutant Spo11F, t=2h)

source_name: IP of H3 occupancy (mutant Spo11F, t=2h in meiosis)


title: ChIP-chip time-course of H3K4me3 during meiosis (mutant clb5Delta-clb6Delta, t=1h)

source_name: IP of H3K4me3 (mutant clb5Delta-clb6Delta, t=1h in meiosis)


title: ChIP-chip time-course of H3K4me3 during meiosis (mutant clb5Delta-clb6Delta, t=4h)

source_name: IP of H3K4me3 (mutant clb5Delta-clb6Delta, t=4h in meiosis)


title: ChIP-chip time-course of H3K4me3 during meiosis (mutant Spo11F, t=6h)

source_name: IP of H3K4me3 (mutant Spo11F, t=6h in meiosis)


title: ChIP-chip time-course of H3 occupancy during meiosis (WT, t=0h)

description: Time-course of  Histone H3 occupancy during meiosis

source_name: IP of H3 occupancy (t=0h in meiosis)

tag: Strain ORD7339


title: ChIP-chip time-course of H3 occupancy during meiosis (WT, t=1h)

source_name: IP of H3 occupancy (t=1h in meiosis)


title: Transcriptomic regulation during meiosis t=8h, Clb5Delta-Clb6Delta mutant

description: Time course of the transcriptomic regulation in the mutant Clb5Delta-Clb6Delta during meiosis, relative to time t=0h.

hyb_protocol: Hybridization with overnight incubation at 63°C on yeast ORFs microarrays and washes were performed as previously described (Borde et al., 2004)

scan_protocol: Scanned with a GenePix 4000A scanner and quantified using GenePix3.0 (Axon Instruments)

data_processing: Ratios of background-substracted intensities were normalized using the Lowess algorithm implemented in BASE (Saal et al, 2002). Ratios were divided by ratios at time t=0h and transformed into log2ratios.

source_name: mRNA extracted at time t=6h

label_protocol: 2 µg of mRNA was used for cDNA synthesis with incorporation of aminoallyl-dUTP (Sigma), then labeled by coupling to N-hydroxysuccinimidyl ester of Cy5 dye (Amersham) as described at http://cat.ucsf.edu/resources/index.html

extract_protocol: Cell samples for RNA extraction were taken by filtration of 40 ml culture on nitrocellulose membranes and immediately frozen in liquid nitrogen. For total RNA extraction, frozen cells stored at –80°C were re-suspended in 1.5 ml TES buffer (10 mM Tris pH 7.5, 10 mM EDTA, 0.5% SDS), 1.5 ml acid phenol/chloroform (5:1) and 0.5 g glass beads. The cells were vortexed vigorously for 1 min, incubated in a 65°C water bath for 1 h with 20 s vortexing every 10 min, placed on ice for 5 min and centrifuged at 1500 g for 5 min. Aqueous phase was removed and 2 to 3 successive acid phenol/chloroform extractions were performed, followed by washing with 1.5 ml chloroform/isoamyl alcohol (25:1). RNA was precipitated in 2 volumes of 95% ethanol and 1/10 volume 3M sodium acetate, re-suspended in DEPC-treated H2O and stored at –80°C. 500 to 1000 µg of total RNA for each sample were used for Poly(A)+ RNA isolation with the Micro-Fast Track 2.0 kit (Invitrogen) following the manufacturer’s protocol for yeast mRNA.

tag: t=8h after meiosis indution

source_name: mRNA meiotic mix

extract_protocol: Same as channel 1

tag: A reference mRNA mix was prepared for each kinetics experiment by pooling equal amounts of mRNA from every time-point of the considered time-course, except for t=0 hr which was added at 4 times the amount of the other samples


title: Transcriptomic regulation during meiosis t=6h, Clb5Delta-Clb6Delta mutant

tag: t=6h after meiosis indution


title: Transcriptomic regulation during meiosis t=5h, Clb5Delta-Clb6Delta mutant

source_name: mRNA extracted at time t=5h

tag: t=5h after meiosis indution


title: Transcriptomic regulation during meiosis t=4h, Clb5Delta-Clb6Delta mutant

source_name: mRNA extracted at time t=4h

tag: t=4h after meiosis indution


title: Transcriptomic regulation during meiosis t=2h, Clb5Delta-Clb6Delta mutant

source_name: mRNA extracted at time t=2h

tag: t=1h after meiosis indution


title: Transcriptomic regulation during meiosis t=1h, Clb5Delta-Clb6Delta mutant

source_name: mRNA extracted at time t=1h


title: storage protein suppression expt, RNAi biol rep2, tech rep1

first: monica

last: schmidt

state: MO

address: 975 n. warson

institute: danforth center

description: storage protein suppression comparison

hyb_protocol: genechip expression analysis technical manual

data_processing: arrayassist software

label: one cycle target, affymetrix part#900493

organism: Glycine max

source_name: 150mg RNAiSP- soybean cotyledon

extract_protocol:
acid-based phenol
Qiagen spin column for cleanup

tag: 150mg RNAiSP cotyledon, greenhouse grown


title: Transcriptomic regulation during meiosis t=6h, Spo11Y135F mutant

description: Time course of the transcriptomic regulation in the mutant Spo11Y135F during meiosis, relative to time t=0h.

tag: Strain ORD6847 (Spo11Y135F mutant)


title: storage protein suppression expt, RNAi biol rep1, tech rep1

description: storage protein suppression comparison

scan_protocol: genechip expression analysis technical manual

source_name: 150mg RNAiSP- cotyledon biol rep 1 tech rep1

tag: 150mg RNAiSP suppressed soybean cotyledon biol rep 1 tech rep1


title: Transcriptomic regulation during meiosis t=8h, Spo11Y135F mutant

source_name: mRNA extracted at time t=8h


title: ChIP-chip time-course of H3 occupancy during meiosis (WT, t=2h)

source_name: IP of H3 occupancy (t=2h in meiosis)

source_name: Whole-cell extract


title: storage protein suppression expt, control tech rep2

description: storage protein suppression comparison

source_name: 150mg nontransgenic soybean cotyledon

label_protocol: genechip expression analysis technical manual

tag: 150mg soybean cotyledon, control tech rep2


title: Transcriptomic regulation during meiosis t=3h, Spo11Y135F mutant

source_name: mRNA extracted at time t=3h

tag: t=3h after meiosis indution


title: Transcriptomic regulation during meiosis t=3h, Clb5Delta-Clb6Delta mutant

tag: Strain ORD6830


title: Transcriptomic regulation during meiosis t=4h, Spo11Y135F mutant


title: Transcriptomic regulation during meiosis t=5h, Spo11Y135F mutant


title: ChIP-chip time-course of H3K4me3 during meiosis (mutant Spo11F, t=2h)

data_processing: Log2Ratios of background-corrected Intensities, spatial bias normalized with MANOR (Neuvial et al. 2006 Bioinformatics) median fitted to 0. Then, we calculated for each time-point the average value of the ratios for probes located between 0 and 500 bp  of all the ORFs present on the array. Next, we calculated the average value of this peak during the whole time-course, and normalized the ratios of each array such that each array has now this average peak value.

source_name: IP of H3K4me3 (mutant Spo11F, t=2h in meiosis)

tag: Strain ORD7341


title: ChIP-chip time-course of H3K4me3 during meiosis (WT, t=4h)

description: Time-course of the trimethylation of the Lysine4 of Histone H3 during meiosis

data_processing: Log2Ratios of background-corrected Intensities, spatial bias normalized with MANOR (Neuvial et al. 2006 Bioinformatics) mean fitted to 0. Then, we calculated for each time-point the average value of the ratios for probes located between 0 and 500 bp (for trimethylation) of all the ORFs present on the array. Next, we calculated the average value of this peak during the whole time-course, and normalized the ratios of each array such that each array has now this average peak value. Finally, we averaged the processed values of the two replicates.

source_name: IP of H3K4me3 (t=4h in meiosis)

extract_protocol: 20ml (4*108 cells) were crosslinked with 1% freshly prepared formaldehyde for 15 min at room temperature, then the reaction was stopped by the addition of 125mM glycin for 5 min. Cells were washed twice with cold TBS, and then chromatin immunoprecipitation was performed as described (Robine et al., 2007), using  3µl of rabbit polyclonal anti-triMe H3K4 (Abcam #Ab8580) and 30 µl protein G magnetic beads suspension (Dynal).

tag: t=4h after meiosis induction


title: Transcriptomic regulation during meiosis t=2h, Spo11Y135F mutant

description: Time course of the transcriptomic regulation during meiosis, relative to time t=0h.

tag: t=2h after meiosis indution


title: ChIP-chip time-course of H3K4me3 during meiosis (WT, t=2h)

source_name: IP of H3K4me3 (t=2h in meiosis)

tag: t=2h after meiosis induction


title: ChIP-chip time-course of H3K4me3 during meiosis (mutant Spo11F, t=1h)

source_name: IP of H3K4me3 (mutant Spo11F, t=1h in meiosis)

tag: t=1h after meiosis induction


title: storage protein suppression expt, RNAi biol rep2, tech rep2

description: storage protein suppression comparison

source_name: 150mg cotyledon RNAiSP biol rep 2 tech rep 2


title: ChIP-chip time-course of H3K4me3 during meiosis (WT, t=1h)

source_name: IP of H3K4me3 (t=1h in meiosis)

tag: Strain ORD7339


title: ChIP-chip time-course of H3K4me3 during meiosis (WT, t=6h)

source_name: IP of H3K4me3 (t=6h in meiosis)

tag: t=6h after meiosis induction


title: ChIP-chip time-course of H3K4me3 during meiosis (WT, t=3h)

source_name: IP of H3K4me3 (t=3h in meiosis)

tag: t=3h after meiosis induction


title: storage protein suppression expt, RNAi biol rep1, tech rep2

description:
3 samples: 1 control, 2 biological samples
jack control, 2 tech replicates
2 RNAi samples, 2 tech replicates each

label: one cycle target labeling, affymetrix 900493

source_name: 150 mg RNAi cotyledon with suppressed storage proteins

extract_protocol:
acid-based phenol
Qiagen spin column for clean-up

tag: 150 mg transgenic soybean cotyledon with both storage proteins suppressed, greenhouse grown


title: Transcriptomic regulation during meiosis t=1h, Spo11Y135F mutant

source_name: mRNA extracted at time t=1h

source_name: mRNA meiotic mix

tag: A reference mRNA mix was prepared for each kinetics experiment by pooling equal amounts of mRNA from every time-point of the considered time-course, except for t=0 hr which was added at 4 times the amount of the other samples


title: storage protein suppression expt, control tech rep1

description: storage protein suppression comparison

source_name: 150mg cotyledon, wt nontransgenic control

tag: 150mg soybean cotyledon, nontransgenic greenhouse grown


title: ChIP-chip time-course of H3K4me3 during meiosis (WT, t=0h)

source_name: IP of H3K4me3 (t=0h in meiosis)

tag: t=0h after meiosis induction


title: Transcriptomic regulation during meiosis t=8h

data_processing: Ratios of background-substracted intensities were normalized using the Lowess algorithm implemented in BASE (Saal et al, 2002). Ratios were divided by ratios at time t=0h and transformed into log2ratios. Log2ratio for the first replicate did not come from an microarray experiment, but has been interpolated from the previous time point of the same experiment.

source_name: mRNA extracted at time t=8h

tag: Strain ORD6822

tag: t=8h after meiosis indution


title: Transcriptomic regulation during meiosis t=6h

source_name: mRNA extracted at time t=6h

tag: t=6h after meiosis indution


title: Transcriptomic regulation during meiosis t=2h

source_name: mRNA extracted at time t=2h


title: Transcriptomic regulation during meiosis t=5h

source_name: mRNA extracted at time t=5h

tag: t=5h after meiosis indution


title: Transcriptomic regulation during meiosis t=4h

source_name: mRNA extracted at time t=4h

tag: t=4h after meiosis indution


title: Transcriptomic regulation during meiosis t=1h

scan_protocol: scanned with a GenePix 4000A scanner and quantified using GenePix3.0 (Axon Instruments)

tag: t=1h after meiosis indution


title: Transcriptomic regulation during meiosis t=3h

source_name: mRNA extracted at time t=3h

tag: t=3h after meiosis indution


title: FAB-SC3

status: Public on Oct 31 2008

city: Boston

first: Niels

last: Geijsen

state: MA

address: 185 Cambridge St. CPZN 4-4256

department: Center for Regenerative Medicine

institute: Massachusetts General Hospital

description: Cells were derived under FAB-SC conditions and 3 separate single cell clones were used for gene expression analysis

hyb_protocol: hybridization to and the washing of the Agilent 4X44K slides was carried out following the manufacturer's protocols

scan_protocol: Scanning was done in an Agilent scanner using the manufacturer's software and protocols(GE1-v5_95_Feb07)

data_processing: Data was processed with the GeneSifter program, normalized to median

source_name: Clonal FAB-SC unstimulated, clone3

label_protocol: cRNAs were amplified and labeled with Cy3 using Agilent's RNA labeling kit

extract_protocol: Total RNA was extracted with Trizol(Invitrogen) following the manufacturer's protocol

tag: Clonal FAB-SC unstimulated, clone3


title: FAB-SC2

source_name: Clonal FAB-SC unstimulated, clone2

tag: Clonal FAB-SC unstimulated, clone2


title: FAB-SC1

source_name: Clonal FAB-SC unstimulated, clone1

tag: Clonal FAB-SC unstimulated, clone1


title: FHA-3 treated PBMC, time point 4Hrs (Experiment Micro#22, sample #22)

status: Public on Oct 30 2008

city: Palo Alto

first: Christine

last: Dieterich

state: CA

address: 3801 Miranda Avenue

department: Department of Microbiology & Immunology

institute: VA hospital

description:
Simple annotation: Bordetella exposure, Filamentous Hemaglutinin (FHA)
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41477.gif
Infection: yes
Time: 4

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 980, 6180; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Christine,,Dieterich Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.56; Parameter Scan Time = 17:17:18; Parameter PMT Volts = 770; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16220; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.61; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.56; Parameter Scan Time = 17:17:18; Parameter PMT Volts = 870; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16219; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.58; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Homo sapiens

source_name: Stratagene Universal Human Reference  RNA amplified 1x using Ambion MessageAmp aRNA kit

label_protocol: not provided

extract_protocol: not provided

source_name: 1 ug total RNA from 4x10E6 FHA-3  treated cells , amplified 1x using Ambion MessageAmp aRNA kit

treatment_protocol: Dieterich_Treatment of human PBMC with purified Bordetella pertussis filamentous hemagglutinin (FHA); Preparation of human peripheral blood mononuclear cells (PBMC)and Bordetella pertussis filamentous hemagglutinin (FHA):Human PBMCs were purified from freshly drawn blood or buffy coat from healthy donors (Stanford Blood Center, Stanford,  CA), using Ficoll-Paque (Amersham Biosciences, Piscataway, N.J.) according to the manufacturer?s instruction. PBMCs were resuspended in RPMI-1640 medium (American Type Culture Collection, ATCC, Manassas, VA) supplemented with 10% fetal bovine serum (ATCC), 100 U/ml penicillin, and 100 ug/ml streptomycin (Gibco, Invitrogen Corportation, Carlsbad, CA). FHA was purified from B. pertussis Bpe160, Bpe162, and Bpe163 and named FHA-2, FHA-3, and FHA-4, respectively, in accordance with a previously described protocol. Briefly, B. pertussis liquid cultures were harvested when the optical density at 600 nm was between 2.5 and 4. The culture supernatant was supplemented with Complete Protease Inhibitor (Roche, Indianapolis, IN) and applied at 2 ml/min on a 5 ml HiTrap Heparin column (Amersham Biosiciences). Purification was performed using an FPLC system equipped with a P-500 pump and a FRAC-P100 fraction collector (Pharmacia LKB). FHA was eluted at 2 ml/min with 1X PBS, 0.5 M NaCl (Mock-2). Total protein concentrations, determined by the BCA test (Pierce, Rockford, IL), were 560, 300, and 340 ug/ml for FHA-2, FHA-3, and FHA-4, respectively. FHA-1 (a kind gift from M. Pizza and R. Rappuoli, Chiron, Sienna, Italy) was isolated from a derivative of B. pertussis, Wellcome 28 (W28) using Matrex Cellufine Sulfate (Millipore) and stored in a solution containing 50% glycerol, 0.5 M NaCl, and 25 mM Na2HPO4 (Mock-1).  PBMC treatment: Cultures comprising 3x106 PBMC were stimulated for 0.5, 2, 4, and 6 hours with 5 ug/ml of each purified B. pertussis FHA. Control PBMC cultures were simultaneously treated with similar volumes of elution buffers (Mock-1 and Mock-2), and sampled at the same time points.; Protocol Type = Biological Sample; Performer: Christine,,Dieterich


title: FHA-1 treated PBMC, time point 4Hrs (Experiment Micro#22, sample #19)

description:
Simple annotation: Bordetella exposure, Filamentous Hemaglutinin (FHA)
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41475.gif
Infection: yes
Time: 4

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 920, 5800; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Christine,,Dieterich Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.47; Parameter Scan Time = 16:35:08; Parameter PMT Volts = 740; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16178; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.61; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.47; Parameter Scan Time = 16:35:08; Parameter PMT Volts = 870; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16177; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.59; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich

tag: Stratagene Universal Human Reference  RNA amplified 1x using Ambion MessageAmp aRNA kit

source_name: 1 ug total RNA from 4x10E6 FHA-1 treated cells , amplified 1x using Ambion MessageAmp aRNA kit


title: FHA-2 treated PBMC, time point 6Hrs (Experiment Micro#22, sample #27)

description:
Simple annotation: Bordetella exposure, Filamentous Hemaglutinin (FHA)
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41481.gif
Infection: yes
Time: 6

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 980, 6180; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Christine,,Dieterich Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.71; Parameter Scan Time = 18:07:20; Parameter PMT Volts = 770; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16270; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.58; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.71; Parameter Scan Time = 18:07:20; Parameter PMT Volts = 870; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16269; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.57; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich

source_name: 1 ug total RNA from 4x10E6 FHA-2 treated cells , amplified 1x using Ambion MessageAmp aRNA kit


title: Mock-1 treated PBMC, time point 6Hrs (Experiment Micro#22, sample #24)

description:
Simple annotation: Bordetella exposure, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41478.gif
Infection: mock-treatment
Time: 6

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 980, 6180; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Christine,,Dieterich Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.65; Parameter Scan Time = 17:32:28; Parameter PMT Volts = 740; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16236; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.60; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.65; Parameter Scan Time = 17:32:28; Parameter PMT Volts = 870; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16235; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.59; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich

source_name: 1 ug total RNA from 4x10E6 Mock-1 treated cells , amplified 1x using Ambion MessageAmp aRNA kit


title: FHA-1 treated PBMC, time point 2Hrs (Experiment Micro#22, sample #13)

description:
Simple annotation: Bordetella exposure, Filamentous Hemaglutinin (FHA)
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41469.gif
Infection: yes
Time: 2

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 920, 5800; Parameter Datafile type = GenePix Results 1.3; Software: type: feature extraction; Performer: Christine,,Dieterich Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.13; Parameter Scan Time = 15:21:34; Parameter PMT Volts = 770; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16105; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.59; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.13; Parameter Scan Time = 15:21:34; Parameter PMT Volts = 880; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16104; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.59; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich

tag: 1 ug total RNA from 4x10E6 FHA-1 treated cells , amplified 1x using Ambion MessageAmp aRNA kit


title: FHA-4 treated PBMC, time point 0.5Hr (Experiment Micro#22, sample #11)

description:
Simple annotation: Bordetella exposure, Filamentous Hemaglutinin (FHA)
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41484.gif
Infection: yes
Time: 0.5

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 920, 5800; Parameter Datafile type = GenePix Results 1.3; Software: type: feature extraction; Performer: Christine,,Dieterich Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.04; Parameter Scan Time = 14:55:23; Parameter PMT Volts = 770; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16078; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.61; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.04; Parameter Scan Time = 14:55:23; Parameter PMT Volts = 910; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16077; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.59; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich

source_name: 1 ug total RNA from 4x10E6 FHA-4  treated cells , amplified 1x using Ambion MessageAmp aRNA kit


title: Untreated PBMC, time point 0 Hr (Experiment Micro#22, sample #2)

description:
Simple annotation: Bordetella exposure, untreated
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41459.gif
Infection: no
Time: 0

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1000, 5880; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Christine,,Dieterich Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.66; Parameter Scan Time = 11:47:33; Parameter PMT Volts = 730; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 15894; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.61; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.66; Parameter Scan Time = 11:47:33; Parameter PMT Volts = 850; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 15893; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.55; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich

source_name: 1 ug total RNA from 4x10E6 untreated cells , amplified 1x using Ambion MessageAmp aRNA kit


title: FHA-3 treated PBMC, time point 0.5Hr (Experiment Micro#22, sample #10)

description:
Simple annotation: Bordetella exposure, Filamentous Hemaglutinin (FHA)
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41467.gif
Infection: yes
Time: 0.5

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 920, 5800; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Christine,,Dieterich Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.95; Parameter Scan Time = 14:26:58; Parameter PMT Volts = 820; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16052; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.61; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.95; Parameter Scan Time = 14:26:58; Parameter PMT Volts = 920; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16050; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.58; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich

tag: 1 ug total RNA from 4x10E6 FHA-3  treated cells , amplified 1x using Ambion MessageAmp aRNA kit


title: Bovine Blastocyst, biological rep2

status: Public on Oct 27 2008

city: Berlin

first: Smita

last: Sudheer

email: sudheer@molgen.mpg.de, adjaye@molgen.mpg.de, kues@tzv.fal.de, niemann@tzv.fal.de

address: Ihnestr. 63-73

country: Germany

institute: Max Planck Institute for Molecular Genetics

description: Gene expression data from preimplantation embryos Blastocyst

hyb_protocol: Ten μg of fragmented cRNA was used for hybridization on the GenChip Bovine Genome Array (Affymetrix) overnight at 45°C according to the manufacture’s instructions.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner.

data_processing: The Bioconductor open source library was used for initial processing of the raw files. CEL files were preprocessed using the GCRMA algorithm of the GCRMA package [v2.0.0] and detection calls were obtained using the mas5calls function of the Affymetrix platform.

label: biotin

molecule: polyA RNA

organism: Bos taurus

source_name: Bovine preimplantation embryo Invivo derived Blastocyst

label_protocol: biotin-labeled cRNA was prepared in an in vitro transcription reaction using the GeneChip IVT Labeling Kit (Affymetrix).

extract_protocol: Poly(A)+ RNA was isolated with a Dynabeads mRNA Direct Kit (Invitrogen) according to the manufacturer's instructions.

tag: In vivo derived

value: Blastocyst


title: FHA-1 treated PBMC, time point 6Hrs (Experiment Micro#22, sample #25)

description:
Simple annotation: Bordetella exposure, Filamentous Hemaglutinin (FHA)
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41479.gif
Infection: yes
Time: 6

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 980, 6180; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Christine,,Dieterich Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.68; Parameter Scan Time = 17:44:08; Parameter PMT Volts = 770; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16247; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.60; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.68; Parameter Scan Time = 17:44:08; Parameter PMT Volts = 870; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16246; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.58; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich


title: Bovine Blastocyst, biological rep3


title: Untreated PBMC, time point 0 Hr, (Experriment Micro#22,  sample #1)

description:
Simple annotation: Bordetella exposure, untreated
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41458.gif
Infection: no
Time: 0

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1000, 5880; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Christine,,Dieterich Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.17; Parameter Scan Time = 11:30:46; Parameter PMT Volts = 700; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 15877; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.61; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.17; Parameter Scan Time = 11:30:46; Parameter PMT Volts = 760; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 15876; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.53; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich

tag: 1 ug total RNA from 4x10E6 untreated cells , amplified 1x using Ambion MessageAmp aRNA kit


title: Mock-2 treated PBMC, time point 4Hrs (Experiment Micro#22, sample #20)

description:
Simple annotation: Bordetella exposure, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41476.gif
Infection: mock-treatment
Time: 4

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 920, 5800; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Christine,,Dieterich Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.50; Parameter Scan Time = 16:48:30; Parameter PMT Volts = 730; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16191; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.60; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.50; Parameter Scan Time = 16:48:30; Parameter PMT Volts = 880; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16190; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.59; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich

source_name: 1 ug total RNA from 4x10E6 Mock-2 treated cells , amplified 1x using Ambion MessageAmp aRNA kit


title: FHA-4 treated PBMC, time point 6Hrs (Experiment Micro#22, sample #29)

description:
Simple annotation: Bordetella exposure, Filamentous Hemaglutinin (FHA)
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41483.gif
Infection: yes
Time: 6

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 980, 6180; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Christine,,Dieterich Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.71; Parameter Scan Time = 18:30:31; Parameter PMT Volts = 750; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16293; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.61; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.71; Parameter Scan Time = 18:30:31; Parameter PMT Volts = 870; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16292; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.57; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich

tag: 1 ug total RNA from 4x10E6 FHA-4  treated cells , amplified 1x using Ambion MessageAmp aRNA kit


title: Mock-1 treated PBMC, time point 4Hrs (Experiment Micro#22, sample #18)

description:
Simple annotation: Bordetella exposure, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41474.gif
Infection: mock-treatment
Time: 4

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 920, 5800; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Christine,,Dieterich Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.41; Parameter Scan Time = 16:23:36; Parameter PMT Volts = 760; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16167; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.60; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.41; Parameter Scan Time = 16:23:36; Parameter PMT Volts = 900; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16165; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.58; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich

tag: 1 ug total RNA from 4x10E6 Mock-1 treated cells , amplified 1x using Ambion MessageAmp aRNA kit


title: FHA-3 treated PBMC, time point 6Hrs (Experiment Micro#22, sample #28)

description:
Simple annotation: Bordetella exposure, Filamentous Hemaglutinin (FHA)
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41482.gif
Infection: yes
Time: 6

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 980, 6180; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Christine,,Dieterich Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.74; Parameter Scan Time = 18:18:51; Parameter PMT Volts = 770; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16282; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.62; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.74; Parameter Scan Time = 18:18:51; Parameter PMT Volts = 870; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16281; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.59; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich


title: Bovine Morula, biological rep3

description: Gene expression data from preimplantation embryos Morula

source_name: Bovine preimplantation embryo Invivo derived Morula

value: Morula


title: FHA-2 treated PBMC, 4Hrs time point (Experiment Micro#22, sample #21)

description:
Simple annotation: Bordetella exposure, Filamentous Hemaglutinin (FHA)
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41485.gif
Infection: yes
Time: 4

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 980, 6180; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Christine,,Dieterich Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.50; Parameter Scan Time = 17:01:03; Parameter PMT Volts = 730; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16203; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.60; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.50; Parameter Scan Time = 17:01:03; Parameter PMT Volts = 860; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16202; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.59; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich

tag: 1 ug total RNA from 4x10E6 FHA-2 treated cells , amplified 1x using Ambion MessageAmp aRNA kit


title: FHA-2 treated PBMC, 0.5Hr (Experiment Micro#22, sample #9)

description:
Simple annotation: Bordetella exposure, Filamentous Hemaglutinin (FHA)
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41466.gif
Infection: yes
Time: 0.5

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 920, 5800; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Christine,,Dieterich Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.67; Parameter Scan Time = 13:45:29; Parameter PMT Volts = 780; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16010; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.62; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.67; Parameter Scan Time = 13:45:29; Parameter PMT Volts = 910; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16009; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.56; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich


title: Mock-1 treated PBMC, time point 0.5Hr (Experiment Micro#22, sample #6)

description:
Simple annotation: Bordetella exposure, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41462.gif
Infection: mock-treatment
Time: 0.5

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 920, 5800; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Christine,,Dieterich Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.16; Parameter Scan Time = 13:01:47; Parameter PMT Volts = 800; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 15967; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.62; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.16; Parameter Scan Time = 13:01:47; Parameter PMT Volts = 900; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 15966; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.58; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich


title: Mock-2 treated PBMC, time point 2Hr (Experiment Micro#22, sample #14)

description:
Simple annotation: Bordetella exposure, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41470.gif
Infection: mock-treatment
Time: 2

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 920, 5800; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Christine,,Dieterich Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.22; Parameter Scan Time = 15:37:06; Parameter PMT Volts = 810; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16120; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.61; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.22; Parameter Scan Time = 15:37:06; Parameter PMT Volts = 880; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16119; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.58; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich

tag: 1 ug total RNA from 4x10E6 Mock-2 treated cells , amplified 1x using Ambion MessageAmp aRNA kit


title: FHA-1 treated PBMC, time point 0.5Hr (Experiment Micro#22, sample #7)

description:
Simple annotation: Bordetella exposure, Filamentous Hemaglutinin (FHA)
Image: http://smd.stanford.edu/MicroArray/gifs//41464.gif
Infection: yes
Time: 0.5

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 920, 5800; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Christine,,Dieterich Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.40; Parameter Scan Time = 13:18:14; Parameter PMT Volts = 900; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 15980; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.55; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich


title: Mock-2 treated PBMC, time point 6Hrs (Experiment Micro#22, sample #26)

description:
Simple annotation: Bordetella exposure, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41480.gif
Infection: mock-treatment
Time: 6

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 980, 6180; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Christine,,Dieterich Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.68; Parameter Scan Time = 17:54:59; Parameter PMT Volts = 770; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16258; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.64; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.68; Parameter Scan Time = 17:54:59; Parameter PMT Volts = 770; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16258; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.64; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich


title: Bovine Morula, biological rep1


title: Bovine 8 Cell, biological rep4

description: Gene expression data from preimplantation embryos 8 Cell

source_name: Bovine preimplantation embryo Invivo derived 8 Cell

value: 8 Cell


title: FHA-4 treated PBMC, time point 2Hrs (Experiment Micro#22, sample #17)

description:
Simple annotation: Bordetella exposure, Filamentous Hemaglutinin (FHA)
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41473.gif
Infection: yes
Time: 2

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 920, 5800; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Christine,,Dieterich Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.35; Parameter Scan Time = 16:12:50; Parameter PMT Volts = 760; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16155; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.60; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.35; Parameter Scan Time = 16:12:50; Parameter PMT Volts = 900; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16154; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.59; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich


title: FHA-3 treated PBMC, time point 2Hrs (Experiment Micro#22, sample #16)

description:
Simple annotation: Bordetella exposure, Filamentous Hemaglutinin (FHA)
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41472.gif
Infection: yes
Time: 2

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 920, 5800; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Christine,,Dieterich Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.35; Parameter Scan Time = 16:02:02; Parameter PMT Volts = 760; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16145; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.61; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.35; Parameter Scan Time = 16:02:02; Parameter PMT Volts = 900; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 16144; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.56; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich


title: Bovine Blastocyst, biological rep1

description: Gene expression data from preimplantation embryos Blastocyst


title: Untreated PBMC, time point 0 Hr (Experiment Micro#22, sample #5)

description:
Simple annotation: Bordetella exposure, untreated
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41461.gif
Infection: no
Time: 0

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 920, 5800; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Christine,,Dieterich Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.97; Parameter Scan Time = 12:47:35; Parameter PMT Volts = 820; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 15952; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.61; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.97; Parameter Scan Time = 12:47:35; Parameter PMT Volts = 890; Parameter Scan Date = 2003-04-29; Parameter Pixel Size = 10; Parameter Laser on time = 15951; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81969]; Parameter Laser Power = 3.58; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Christine,,Dieterich